Why times are 00:00 when trying to plot them using matplotlib?

This is because DateFormatter removes the floating point from the ordinal value of your date:

~/.local/bin/anaconda3/lib/python3.7/site-packages/matplotlib/dates.py in _from_ordinalf(x, tz)
    281         tz = _get_rc_timezone()
    282 
--> 283     ix, remainder = divmod(x, 1)
    284     ix = int(ix)
    285     if ix < 1:

You have to create your own ticks/ticklabels with ax.set_yticks or preferably ax.set_yticklabels

You could slice the times in a list comprehension:

import datetime as dt
import matplotlib.pyplot as plt
from matplotlib.dates import DateFormatter

datetimes_str = ['2020-08-03T03:46:18.000Z', '2020-08-01T01:14:31.000Z',
                 '2020-07-27T22:45:11.000Z', '2020-07-21T20:00:42.000Z',
                 '2020-07-20T00:37:17.000Z', '2020-07-16T00:40:47.000Z']

datetimes = [dt.datetime.strptime(d, "%Y-%m-%dT%H:%M:%S.%fZ") for d in datetimes_str]
times = sorted([d[11:16] for d in datetimes_str])

fig, ax = plt.subplots()
ax.plot(datetimes, times)
ax.xaxis.set_major_formatter(DateFormatter('%Y/%m/%d'))
fig.autofmt_xdate()
plt.show()

Producing:

This happens because the only thing that is different for the x and y axis is the format for representing the dateTime, not the value of the dateTime itself, that's why you will always get a diagonal line.

So the 00:00 are just shown since the values for the y axis are too varies to precisely represent the hours.

In order to change this you would need to change the value for the y axis by removing the date information and keeping only the time. Here is a code snippet that should do the trick:

import datetime as dt
import matplotlib.pyplot as plt
from matplotlib.dates import DateFormatter, DayLocator, HourLocator

datetimes_str = ['2020-08-03T03:46:18.000Z', '2020-08-01T01:14:31.000Z',
                 '2020-07-27T22:45:11.000Z', '2020-07-21T20:00:42.000Z',
                 '2020-07-20T00:37:17.000Z', '2020-07-16T00:40:47.000Z']

datetimes = [dt.datetime.strptime(d, "%Y-%m-%dT%H:%M:%S.%fZ") for d in datetimes_str]
times = [d.replace(day=1, month=1, year=2000) for d in datetimes]

# The above list contains datetimes:
# 2020-08-03 03:46:18
# 2020-08-01 01:14:31
# 2020-07-27 22:45:11
# 2020-07-21 20:00:42
# 2020-07-20 00:37:17
# 2020-07-16 00:40:47

fig, ax = plt.subplots()

ax.yaxis.set_major_formatter(DateFormatter('%H:%M'))
ax.xaxis.set_major_formatter(DateFormatter('%Y/%m/%d'))

ax.plot(datetimes, times)

fig.autofmt_xdate()

plt.show()